I agree, I almost always and instinctively palm mute to some extent, hard not to. But to each his own. I also dont down tune. I also loooove the axe. For the record.in testing and using riff 1, the clarity of the a string is the same between my diezel vh4s and my axe-fx using the diezel amp.
with both i find it better to mute the open d string when playing the a string notes. i know the tab is written as d string open, but in performance, are you muting the d string when you do the a string hammers? that instantly makes the notes clearer using both the amp and the axe.
i have a little more time to experiment. i'm just having the same difficulty with both amps. i know with the axe, though, i have many options for fixing it where as with the amp i only have 6 or so knobs.